11-19210493-CTTTTTTTTT-CTTTTTTTTTT

Variant names:

• chr11-19210493-C-CT
• rs34865888
• ENST00000533783.2:c.-162dupA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000533783.2(CSRP3):​c.-162dupA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.012 (15 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CSRP3 ENST00000533783.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

CSRP3 (HGNC:2472): (cysteine and glycine rich protein 3) This gene encodes a member of the CSRP family of LIM domain proteins, which may be involved in regulatory processes important for development and cellular differentiation. The LIM/double zinc-finger motif found in this protein is found in a group of proteins with critical functions in gene regulation, cell growth, and somatic differentiation. Mutations in this gene are thought to cause heritable forms of hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in humans. Alternatively spliced transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0123 (1221/98886) while in subpopulation AFR AF= 0.0302 (901/29800). AF 95% confidence interval is 0.0286. There are 15 homozygotes in gnomad4. There are 540 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRP3-AS1	NR_183675.1	n.207+13593dupT		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRP3	ENST00000533783.2	c.-162dupA		5_prime_UTR_variant	Exon 1 of 7	1		ENSP00000431813.1
CSRP3-AS1	ENST00000527978.1	n.145+13593dupT		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1218 AN: 98906 Hom.: 15 Cov.: 0

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00807

Gnomad ASJ AF: 0.00123

Gnomad EAS AF: 0.00144

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.00870

Gnomad NFE AF: 0.00465

Gnomad OTH AF: 0.0113

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0123 AC: 1221 AN: 98886 Hom.: 15 Cov.: 0 AF XY: 0.0116 AC XY: 540 AN XY: 46614

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.00807

Gnomad4 ASJ AF: 0.00123

Gnomad4 EAS AF: 0.00144

Gnomad4 SAS AF: 0.00251

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.00465

Gnomad4 OTH AF: 0.0112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34865888; hg19: chr11-19232040;